Generic placeholder image

Current Medicinal Chemistry

Editor-in-Chief

ISSN (Print): 0929-8673
ISSN (Online): 1875-533X

Review Article

Technological Advances in Preclinical Drug Evaluation: The Role of -Omics Methods

Author(s): Sandra Kraljević Pavelić*, Elitza Markova-Car, Marko Klobučar, Lana Sappe and Radan Spaventi

Volume 27, Issue 8, 2020

Page: [1337 - 1349] Pages: 13

DOI: 10.2174/0929867326666190711122819

Price: $65

Abstract

Preclinical drug development is an essential step in the drug development process where the evaluation of new chemical entities occurs. In particular, preclinical drug development phases include deep analysis of drug candidates’ interactions with biomolecules/targets, their safety, toxicity, pharmacokinetics, metabolism by use of assays in vitro and in vivo animal assays. Legal aspects of the required procedures are well-established. Herein, we present a comprehensive summary of current state-of-the art approaches and techniques used in preclinical studies. In particular, we will review the potential of new, -omics methods and platforms for mechanistic evaluation of drug candidates and speed-up of the preclinical evaluation steps.

Keywords: Drug testing, proteomics, transcriptomics, mass spectrometry, preclinical drug evaluation, -omics methods.

[1]
Owens, P.K.; Raddad, E.; Miller, J.W.; Stille, J.R.; Olovich, K.G.; Smith, N.V.; Jones, R.S.; Scherer, J.C. A decade of innovation in pharmaceutical R&D: the Chorus model. Nat. Rev. Drug Discov., 2015, 14(1), 17-28.
[http://dx.doi.org/10.1038/nrd4497] [PMID: 25503514]
[2]
Morgan, P.; Brown, D.G.; Lennard, S.; Anderton, M.J.; Barrett, J.C.; Eriksson, U.; Fidock, M.; Hamrén, B.; Johnson, A.; March, R.E.; Matcham, J.; Mettetal, J.; Nicholls, D.J.; Platz, S.; Rees, S.; Snowden, M.A.; Pangalos, M.N. Impact of a five-dimensional framework on R&D productivity at AstraZeneca. Nat. Rev. Drug Discov., 2018, 17(3), 167-181.
[http://dx.doi.org/10.1038/nrd.2017.244] [PMID: 29348681 ]
[3]
Erakovic Haber, V.; Spaventi, R. Blue Biotechnology, Progress in Molecular and Subcellular Biology 55; Werner, E.; Müller, G.; Schröder, H.C; Wang, X., Ed.; Springer International Publishing AG, 2017, pp. 91-104.
[4]
ICH guideline S6 (R1) - preclinical safety evaluation of biotechnology-derived pharmaceuticals http://www.ema.europa.eu/docs/en_GB/document_ library/Scientific_guideline/2009/09/WC500002828.pdf (Accessed date: 6 june 2019)
[5]
Dihazi, H.; Asif, A.R.; Beissbarth, T.; Bohrer, R.; Feussner, K.; Feussner, I.; Jahn, O.; Lenz, C.; Majcherczyk, A.; Schmidt, B.; Schmitt, K.; Urlaub, H.; Valerius, O. Integrative omics-from data to biology. Expert Rev. Proteomics, 2018, 15(6), 463-466.
[6]
Verdier, F. Biotechnology and Safety AssessmentThomas, J.A; Fuchs, R.L., Ed.; Elsevier Inc, 2003, pp. 397-412.
[http://dx.doi.org/10.1080/14789450.2018.1476143]
[7]
Pilling, A.M. The role of the toxicologic pathologist in the preclinical safety evaluation of biotechnology-derived pharmaceuticals. Toxicol. Pathol., 1999, 27(6), 678-688.
[http://dx.doi.org/10.1177/019262339902700610] [PMID: 10588549]
[8]
Li, W.; Lam, M.; Choy, D.; Birkeland, A.; Sullivan, M.E.; Post, J.M. Human primary renal cells as a model for toxicity assessment of chemo-therapeutic drugs. Toxicol. In Vitro, 2006, 20(5), 669-676.
[http://dx.doi.org/10.1016/j.tiv.2005.09.016] [PMID: 16289493 ]
[9]
Li, A.P.; Bode, C.; Sakai, Y. A novel in vitro system, the integrated discrete multiple organ cell culture (IdMOC) system, for the evaluation of human drug toxicity: comparative cytotoxicity of tamoxifen towards normal human cells from five major organs and MCF-7 adenocarcinoma breast cancer cells. Chem. Biol. Interact., 2004, 150(1), 129-136.
[http://dx.doi.org/10.1016/j.cbi.2004.09.010] [PMID: 15522266 ]
[10]
Davis, M.; Boekelheide, K.; Boverhof, D.R.; Eichenbaum, G.; Hartung, T.; Holsapple, M.P.; Jones, T.W.; Richard, A.M.; Watkins, P.B. The new revolution in toxicology: the good, the bad, and the ugly. Ann. N. Y. Acad. Sci., 2013, 1278, 11-24.
[http://dx.doi.org/10.1111/nyas.12086] [PMID: 23488558 ]
[11]
Tomaszewski, J.E. Multi-species toxicology approaches for oncology drugs: the US perspective. Eur. J. Cancer, 2004, 40(6), 907-913.
[http://dx.doi.org/10.1016/j.ejca.2003.11.024] [PMID: 15120046 ]
[12]
Kraljevic, S.; Stambrook, P.J.; Pavelic, K. Accelerating drug discovery. EMBO Rep., 2004, 5(9), 837-842.
[http://dx.doi.org/10.1038/sj.embor.7400236] [PMID: 15470377 ]
[13]
Bierly, A. The expanding role of PCR in research and medicine. MLO Med. Lab. Obs., 2012, 44(5), 24-26,26.
[PMID: 22649966 ]
[14]
Goodsaid, F. Quantitative real time polymerase chain reaction in drug development. Drug Dev. Res., 2004, 62(2), 151-158.
[http://dx.doi.org/10.1002/ddr.10378]
[15]
Arikawa, E.; Prabhakar, S.; Zhang, H.; You, M. RT2 Profiler PCR Array application examples: pathway-focused gene expression profiling in toxicology, oncology, and immunology research; QIAGEN, 2012, pp. 1-10.
[16]
AbuHammad, S.; Zihlif, M. Gene expression alterations in doxorubicin resistant MCF7 breast cancer cell line. Genomics, 2013, 101(4), 213-220.
[http://dx.doi.org/10.1016/j.ygeno.2012.11.009] [PMID: 23201559]
[17]
Amatori, S.; Persico, G.; Fanelli, M. Real-time quantitative PCR array to study drug-induced changes of gene expression in tumor cell lines. J. Cancer Metastasis Treat., 2017, 3, 90-99.
[18]
Lohmann, S.; Herold, A.; Bergauer, T.; Belousov, A.; Betzl, G.; Demario, M.; Dietrich, M.; Luistro, L.; Poignée-Heger, M.; Schostack, K.; Simcox, M.; Walch, H.; Yin, X.; Zhong, H.; Weisser, M. Gene expression analysis in biomarker research and early drug development using function tested reverse transcription quantitative real-time PCR assays. Methods, 2013, 59(1), 10-19.
[http://dx.doi.org/10.1016/j.ymeth.2012.07.003] [PMID: 22796720]
[19]
Halait, H.; Demartin, K.; Shah, S.; Soviero, S.; Langland, R.; Cheng, S.; Hillman, G.; Wu, L.; Lawrence, H.J. Analytical performance of a real-time PCR-based assay for V600 mutations in the BRAF gene, used as the companion diagnostic test for the novel BRAF inhibitor vemurafenib in metastatic melanoma. Diagn. Mol. Pathol., 2012, 21(1), 1-8.
[http://dx.doi.org/10.1097/PDM.0b013e31823b216f] [PMID: 22306669 ]
[20]
Gomase, V.S.; Tagore, S.; Kale, K.V. Microarray: an approach for current drug targets. Curr. Drug Metab., 2008, 9(3), 221-231.
[http://dx.doi.org/10.2174/138920008783884795] [PMID: 18336225]
[21]
a)Debouck, C.; Goodfellow, P.N. DNA microarrays in drug discovery and development. Nature genetics. Nat. Genet., 1999, 21, 48-50.
[http://dx.doi.org/10.1038/4475] [PMID: 9915501 ]
b)P. A. Clarke, R. T. Poele, R. Wooster, P. Workman. Biochem. Pharmacol., 2001, 62(10), 1311-1336.
[http://dx.doi.org/10.1016/s0006-2952(01)00785-7] [PMID: 11709192 ]
[22]
Ushijima, M.; Mashima, T.; Tomida, A.; Dan, S.; Saito, S.; Furuno, A.; Tsukahara, S.; Seimiya, H.; Yamori, T.; Matsuura, M. Development of a gene expression database and related analysis programs for evaluation of anticancer compounds. Cancer Sci., 2013, 104(3), 360-368.
[http://dx.doi.org/10.1111/cas.12071] [PMID: 23176546 ]
[23]
Li, C.C.; Lo, H.Y.; Hsiang, C.Y.; Ho, T.Y. DNA microarray analysis as a tool to investigate the therapeutic mechanisms and drug development of Chinese medicinal herbs. BioMedicine. Biomed, 2012, 2, 10-16.
[http://dx.doi.org/10.1016/j.biomed.2012.02.002]
[24]
Buszczak, M.; Signer, R.A.; Morrison, S.J. Cellular differences in protein synthesis regulate tissue homeostasis. Cell, 2014, 159(2), 242-251.
[http://dx.doi.org/10.1016/j.cell.2014.09.016] [PMID: 25303523]
[25]
a)Hetz, C.; Chevet, E. H. P. Harding HP. Targeting the unfolded protein response in disease. Nat. Rev. Drug Discov., 2013, 12(9), 703-719.
[http://dx.doi.org/10.1038/nrd3976] [PMID: 23989796 ]
b) T. M. Karve, A. K. Cheema J. Small changes huge impact: the role of protein posttranslational modifications in cellular homeostasis and disease. Amino Acids, 2011.
[26]
Altelaar, A.F.; Munoz, J.; Heck, A.J. Next-generation proteomics: towards an integrative view of proteome dynamics. Nat. Rev. Genet., 2013, 14(1), 35-48.
[http://dx.doi.org/10.1038/nrg3356] [PMID: 23207911 ]
[27]
a)Walgren, J.L.; Thompson, D.C. Application of proteomic technologies in the drug development process. Toxicol. Lett., 2004, 149(1-3), 377-385.
[http://dx.doi.org/10.1016/j.toxlet.2003.12.047] [PMID: 15093284]
b)Wang, Y.; Chiu, J.F.; He, Q.Y. Proteomics approach to illustrate drug action mechanisms. Current drug discovery technologies. Curr. Drug Discov. Technol., 2006, 3(3), 199-209.
[http://dx.doi.org/10.2174/157016306780136763] [PMID: 17311565]
[28]
Patterson, S.D.; Aebersold, R.H. Proteomics: the first decade and beyond. Nat. Genet., 2003, 33(33)(Suppl.), 311-323.
[http://dx.doi.org/10.1038/ng1106] [PMID: 12610541]
[29]
Barbosa, E.B.; Vidotto, A.; Polachini, G.M.; Henrique, T.; Marqui, A.B.; Tajara, E.H. Proteomics: methodologies and applications to the study of human diseases Rev Assoc Med Bras (1992),, 2012, 58(3), 366-375.
[PMID: 22735231]
[30]
Wang, J.H.; Hewick, R.M. Proteomics in drug discovery. Drug Discov. Today, 1999, 4(3), 129-133.
[http://dx.doi.org/10.1016/S1359-6446(99)01306-9] [PMID: 10322265]
[31]
a)Rabilloud, T.; Chevallet, M.; Luche, S.; Lelong, C. Two-dimensional gel electrophoresis in proteomics: Past, present and future. Lelong, C. J.of Proteomics, 2010, 73(11), 2064-2077.
bLarbi, N.B.; and Jefferies, C. 2009 2D-DIGE: comparative proteomics of cellular signalling pathways. Methods in Mol. Biol., 2009, 517, 105-132.
[32]
Massion, P.P.; Caprioli, R.M. Proteomic strategies for the characterization and the early detection of lung cancer. J. Thorac. Oncol., 2006, 1(9), 1027-1039.
[http://dx.doi.org/10.1016/S1556-0864(15)31639-7] [PMID: 17409991]
[33]
Ummanni, R.; Mundt, F.; Pospisil, H.; Venz, S.; Scharf, C.; Barett, C.; Fälth, M.; Köllermann, J.; Walther, R.; Schlomm, T.; Sauter, G.; Bokemeyer, C.; Sültmann, H.; Schuppert, A.; Brümmendorf, T.H.; Balabanov, S. Identification of clinically relevant protein targets in prostate cancer with 2D-DIGE coupled mass spectrometry and systems biology network platform. PLoS One, 2011, 6(2)e16833
[http://dx.doi.org/10.1371/journal.pone.0016833] [PMID: 21347291 ]
[34]
Lino, M.A.M.; Palacios-Rodriguez, Y.; Rodriguez-Cuevas, S.; Bautista-Pina, V.; Marchat, L.A.; Ruiz-Garcia, E.; Astudillo-de la Vega, H.; Gonzalez-Santiago, A.E.; Flores-Perez, A.; Diaz-Chavez, J.; Carlos-Reyes, A.; Alvarez-Sanchez, E. Lopez-Camarillo. Comparative proteomic profiling of triple-negative breast cancer reveals that up-regulation of RhoGDI-2 is associated to the inhibition of caspase 3 and caspase 9. C. J. Proteomics, 2014, 111, 198-211.
[http://dx.doi.org/10.1016/j.jprot.2014.04.019] [PMID: 24768906]
[35]
Zhang, J.T.; Liu, Y. Use of comparative proteomics to identify potential resistance mechanisms in cancer treatment. Cancer Treat. Rev., 2007, 33(8), 741-756.
[http://dx.doi.org/10.1016/j.ctrv.2007.07.018] [PMID: 17854999 ]
[36]
a)Wang, Y.; He, Q.Y.; Che, C.M.; Chiu, J.F. Proteomic characterization of the cytotoxic mechanism of gold (III) porphyrin 1a, a potential anticancer drug. Proteomics, 2006, 6(1), 131-142.
b)MacKeigan, J.P.; Clements, C.M.; Lich, J.D.; Pope, R.M.; Hod, Y.; Ting, J.P. Proteomic profiling drug-induced apoptosis in non-small cell lung carcinoma: identification of RS/DJ-1 and RhoGDIα. Cancer research. Cancer Res., 2003, 63(20), 6928-6934.
[PMID: 14583493]
[37]
Li, W.R.; Shi, Q.S.; Dai, H.Q.; Liang, Q.; Xie, X.B.; Huang, X.M.; Zhao, G.Z.; Zhang, L.X. Antifungal activity, kinetics and molecular mechanism of action of garlic oil against Candida albicans. Sci. Rep., 2016, 6, 22805.
[http://dx.doi.org/10.1038/srep22805] [PMID: 26948845 ]
[38]
Isbell, M.A.; Morin, D.; Boland, B.; Buckpitt, A.; Salemi, M.; Presley, J. Identification of proteins adducted by reactive naphthalene metabolites in vitro. Proteomics, 2005, 5(16), 4197-4204.
[http://dx.doi.org/10.1002/pmic.200401278] [PMID: 16206326]
[39]
Magdeldin, S.; Enany, S.; Yoshida, Y.; Xu, B.; Zhang, Y.; Zureena, Z.; Lokamani, I.; Yaoita, E.; Yamamoto, T. Basics and recent advances of two dimensional-polyacrylamide gel electrophoresis. Clin. Proteomics, 2014, 11.
[40]
a)Pan, S.; Aebersold, R. Quantitative proteomics by stable isotope labeling and mass spectrometry. Methods in Mol. Biol., 2007, 367, 209-218.
[http://dx.doi.org/10.1038/nprot.2006.22]
b)Wong, JW.; Cagney, G. An overview of label-free quantitation methods in proteomics by mass spectrometry. Cagney. Methods Mol. Biol., 2010, 604, 273-283.
[http://dx.doi.org/10.1007/978-1-60761-444-9-18]
[41]
a)Shiio, Y.; Aebersold, R. Quantitative proteome analysis using isotope-coded affinity tags and mass spectrometry. Nat. Protoc., 2006, 1(1), 139-145.
b)Boersema, P.J.; Raijmakers, R.; Lemeer, S.; Mohammed, S.; Heck, A.J. Multiplex peptide stable isotope dimethyl labeling for quantitative proteomics. Nat. Protoc., 2009, 4(4), 484-494.
[PMID: 19300442]
[42]
Ye, X.; Luke, B.; Andresson, T.; Blonder, J. Brief. Funct. Genomics Proteomics, 2009, 8(2), 136-144.
[http://dx.doi.org/10.1093/bfgp/eln055]
[43]
Ong, S.E.; Blagoev, B.; Kratchmarova, I.; Kristensen, D.B.; Steen, H.; Pandey, A.; Mann, M. Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol. Cell. Proteomics, 2002, 1(5), 376-386.
[http://dx.doi.org/10.1074/mcp.M200025-MCP200] [PMID: 12118079]
[44]
Li, Z.; Adams, R.M.; Chourey, K.; Hurst, G.B.; Hettich, R.L.; Pan, C. Systematic comparison of label-free, metabolic labeling, and isobaric chemical labeling for quantitative proteomics on LTQ Orbitrap Velos. J. Proteome Res., 2012, 11(3), 1582-1590.
[http://dx.doi.org/10.1021/pr200748h] [PMID: 22188275 ]
[45]
Lobo, M.D.; Moreno, F.B.; Souza, G.H.; Verde, S.M.; Moreira, R.A.; Monteiro-Moreira, A.C. Label-Free Proteome Analysis of Plasma from Patients with Breast Cancer: Stage Specific Protein Expression. Front. Oncol., 2017, 7, 14.
[http://dx.doi.org/10.3389/fonc.2017.00014] [PMID: 28210565 ]
[46]
a)E. J. Lee, S. H. Kim, Y. E. Kwark, J. Kim, Exp. Mol. Med., 2006, 38(3), 203-209.
b)J. R. Lou, N. Fatima, Z. Xiao, S. Stauffer, G. Smythers, P. Greenwald, I. U. Ali. Cancer Epidem Biomar, 2006, 15(9), 1598-1606.
[47]
Dazert, E.; Colombi, M.; Boldanova, T.; Moes, S.; Adametz, D.; Quagliata, L.; Roth, V.; Terracciano, L.; Heim, M.H.; Jenoe, P.; Hall, M.N. Quantitative proteomics and phosphoproteomics on serial tumor biopsies from a sorafenib-treated HCC patient. Proc. Natl. Acad. Sci. USA, 2016, 113(5), 1381-1386.
[http://dx.doi.org/10.1073/pnas.1523434113] [PMID: 26787912 ]
[48]
Moellering, R.E.; Cravatt, B.F. How chemoproteomics can enable drug discovery and development. Chem. Biol., 2012, 19(1), 11-22.
[http://dx.doi.org/10.1016/j.chembiol.2012.01.001] [PMID: 22284350]
[49]
Bantscheff, M.; Drewes, G. Chemoproteomic approaches to drug target identification and drug profiling. Bioorg. Med. Chem., 2012, 20(6), 1973-1978.
[http://dx.doi.org/10.1016/j.bmc.2011.11.003] [PMID: 22130419 ]
[50]
Cravatt, B.F.; Wright, A.T.; Kozarich, J.W. Activity-based protein profiling: from enzyme chemistry to proteomic chemistry. Annu. Rev. Biochem., 2008, 77, 383-414.
[http://dx.doi.org/10.1146/annurev.biochem.75.101304.124125] [PMID: 18366325]
[51]
Ong, S.E.; Schenone, M.; Margolin, A.A.; Li, X.; Do, K.; Doud, M.K.; Mani, D.R.; Kuai, L.; Wang, X.; Wood, J.L.; Tolliday, N.J.; Koehler, A.N.; Marcaurelle, L.A.; Golub, T.R.; Gould, R.J.; Schreiber, S.L.; Carr, S.A. Identifying the proteins to which small-molecule probes and drugs bind in cells. Proc. Natl. Acad. Sci. USA, 2009, 106(12), 4617-4622.
[http://dx.doi.org/10.1073/pnas.0900191106] [PMID: 19255428]
[52]
Huang, S.M.A.; Mishina, Y.M.; Liu, S.; Cheung, A.; Stegmeier, F.; Michaud, G.A.; Charlat, O.; Wiellette, E.; Zhang, Y.; Wiessner, S.; Hild, M.; Shi, X.; Wilson, C.J.; Mickanin, C.; Myer, V.; Fazal, A.; Tomlinson, R.; Serluca, F.; Shao, W.; Cheng, H.; Shultz, M.; Rau, C.; Schirle, M.; Schlegl, J.; Ghidelli, S.; Fawell, S.; Lu, C.; Curtis, D.; Kirschner, M.W.; Lengauer, C.; Finan, P.M.; Tallarico, J.A.; Bouwmeester, T.; Porter, J.A.; Bauer, A.; Cong, F. Tankyrase inhibition stabilizes axin and antagonizes Wnt signalling. Nature, 2009, 461(7264), 614-620.
[http://dx.doi.org/10.1038/nature08356] [PMID: 19759537]
[53]
a)Shi, H.; Zhang, C.J.; Chen, G.Y.; Yao, S.Q. Cell-based proteome profiling of potential dasatinib targets by use of affinity-based probes. J. Am. Chem. Soc., 2012, 134(6), 3001-3014.
[http://dx.doi.org/10.1021/ja208518u] [PMID: 22242683 ]
b)Moulick, K.; Ahn, J.H. l Zong, H.; Rodina, A.; Cerchietti, L.; Gomes, E.M.; Caldas-Lopes, E.; Beebe, K.; Perna, F.; Hatzi, K.; Vu, L.P.; Zhao, X.; Zatorska, D.; Taldone, T.; Smith-Jones, P.; Alpaugh, M.; Gross, S.S.; Pillarsetty, N.; Ku, T.; Lewis, J.S.; Larson, S.M.; Levine, R.; Erdjument-Bromage, H.; Guzman, M.L.; Nimer, S.D.; Melnick, A.; Neckers, L.; Chiosis, G. Affinity-based proteomics reveal cancer-specific networks coordinated by Hsp90. Nat. Chem. Biol., 2011, 7(11), 818.
[http://dx.doi.org/10.1038/nchembio.670] [PMID: 21946277]
[54]
Fischer, J.J.; Graebner Baessler, O.Y.; Dalhoff, C.; Michaelis, S.; Schrey, A.K.; Ungewiss, J.; Andrich, K.; Jeske, D.; Kroll, F.; Glinski, M.; Sefkow, M.; Dreger, M.; Koester, H. Comprehensive identification of staurosporine-binding kinases in the hepatocyte cell line HepG2 using Capture Compound Mass Spectrometry (CCMS). J. Proteome Res., 2010, 9(2), 806-817.
[http://dx.doi.org/10.1021/pr9007333] [PMID: 20028079 ]
[55]
Salisbury, C.M.; Cravatt, B.F. Optimization of activity-based probes for proteomic profiling of histone deacetylase complexes. J. Am. Chem. Soc, 2008, 130(7), 2184-2194.
[http://dx.doi.org/10.1021/ja074138u] [PMID: 18217751 ]
[56]
a) M. Y. Pai, B. Lomenick, H. Hwang, R. Schiestl, W.McBride, J. A. Loo, J. Huang, Chemical Biology. Methods Protoc., 2015, 1263, 287-298.
b)E. C. Strickland, M. A. Geer, D. T. Tran, J. Adhikari, G.M. West, P. D. DeArmond, Y. Xu, M. C. Nat. Protoc., 2013, 8(1), 148-161.
[http://dx.doi.org/10.1038/nprot.2012.146] [PMID: 23257983]
[57]
Chang, J.; Kim, Y.; Kwon, H.J. Advances in identification and validation of protein targets of natural products without chemical modification. Nat. Prod. Rep., 2016, 33(5), 719-730.
[http://dx.doi.org/10.1039/C5NP00107B] [PMID: 26964663]
[58]
Lomenick, B.; Olsen, R.W.; Huang, J. Identification of direct protein targets of small molecules. ACS Chem. Biol., 2011, 6(1), 34-46.
[http://dx.doi.org/10.1021/cb100294v] [PMID: 21077692]
[59]
West, G.M.; Tucker, C.L.; Xu, T.; Park, S.K.; Han, X.; Yates, J.R., III; Fitzgerald, M.C. Quantitative proteomics approach for identifying protein-drug interactions in complex mixtures using protein stability measurements. Proc. Natl. Acad. Sci. USA, 2010, 107(20), 9078-9082.
[http://dx.doi.org/10.1073/pnas.1000148107] [PMID: 20439767 ]
[60]
Lomenick, B.; Hao, R.; Jonai, N.; Chin, R.M.; Aghajan, M.; Warburton, S.; Wang, J.; Wu, R.P.; Gomez, F.; Loo, J.A.; Wohlschlegel, J.A.; Vondriska, T.M.; Pelletier, J.; Herschman, H.R.; Clardy, J.; Clarke, C.F.; Huang, J. Target identification using drug affinity responsive target stability (DARTS). Proc. Natl. Acad. Sci. USA, 2009, 106(51), 21984-21989.
[http://dx.doi.org/10.1073/pnas.0910040106] [PMID: 19995983 ]
[61]
Hultschig, C.; Kreutzberger, J.; Seitz, H.; Konthur, Z.; Büssow, K.; Lehrach, H. Recent advances of protein microarrays. Curr. Opin. Chem. Biol., 2006, 10(1), 4-10.
[http://dx.doi.org/10.1016/j.cbpa.2005.12.011] [PMID: 16376134 ]
[62]
Romanov, V.; Davidoff, S.N.; Miles, A.R.; Grainger, D.W.; Gale, B.K.; Brooks, B.D. A critical comparison of protein microarray fabrication technologies. Analyst (Lond.), 2014, 139(6), 1303-1326.
[http://dx.doi.org/10.1039/C3AN01577G]
[63]
Cha, T.; Guo, A.; Zhu, X.Y. Enzymatic activity on a chip: the critical role of protein orientation. Proteomics, 2005, 5(2), 416-419.
[http://dx.doi.org/10.1002/pmic.200400948] [PMID: 15627963 ]
[64]
Chao, G.; Lau, W.L.; Hackel, B.J.; Sazinsky, S.L.; Lippow, S.M.; Wittrup, K.D. Isolating and engineering human antibodies using yeast surface display. Nat. Protoc., 2006, 1(2), 755-768.
[http://dx.doi.org/10.1038/nprot.2006.94] [PMID: 17406305]
[65]
Ramachandran, N.; Raphael, J.V.; Hainsworth, E.; Demirkan, G.; Fuentes, M.G.; Rolfs, A.; Hu, Y.; LaBaer, J. Next-generation high-density self-assembling functional protein arrays. Nat. Methods, 2008, 5(6), 535-538.
[http://dx.doi.org/10.1038/nmeth.1210] [PMID: 18469824 ]
[66]
He, M.; Stoevesandt, O.; Palmer, E.A.; Khan, F.; Ericsson, O.; Taussig, M.J. Printing protein arrays from DNA arrays. Nat. Methods, 2008, 5(2), 175-177.
[http://dx.doi.org/10.1038/nmeth.1178] [PMID: 18204456 ]
[67]
He, M.; Taussig, M.J. Single step generation of protein arrays from DNA by cell-free expression and in situ immobilisation (PISA method). Nucleic Acids Res., 2001, 29(15), E73-E3.
[http://dx.doi.org/10.1093/nar/29.15.e73] [PMID: 11470888 ]
[68]
Qiu, J.; LaBaer, J. Nucleic acid programmable protein array a just-in-time multiplexed protein expression and purification platform. Methods Enzymol., 2011, 500, 151-163.
[http://dx.doi.org/10.1016/B978-0-12-385118-5.00009-8] [PMID: 21943897 ]
[69]
Ray, S.; Mehta, G.; Srivastava, S. Label-free detection techniques for protein microarrays: prospects, merits and challenges. Proteomics, , 2010, 10(4), 731-748.
[http://dx.doi.org/10.1002/pmic.200900458] [PMID: 19953541 ]
[70]
Espina, V.; Woodhouse, E.C.; Wulfkuhle, J.; Asmussen, H.D.; Petricoin, E.F., III; Liotta, L.A. Protein microarray detection strategies: focus on direct detection technologies. J. Immunol. Methods, 2004, 290(1-2), 121-133.
[http://dx.doi.org/10.1016/j.jim.2004.04.013] [PMID: 15261576 ]
[71]
Shao, W.; Zhou, Z.; Laroche, I.; Lu, H.; Zong, Q.; Patel, D.D.; Kingsmore, S.; Piccoli, S.P. Optimization of rolling-circle amplified protein microarrays for multiplexed protein profiling. J. Biomed. Biotechnol., 2003, 2003(5), 299-307.
[http://dx.doi.org/10.1155/S1110724303209268] [PMID: 14688416 ]
[72]
Brase, J.C.; Mannsperger, H.; Frohlich, H.; Gade, S.; Schmidt, C.; Wiemann, S.; Beissbarth, T.; Schlomm, T.; Sultmann, H.; Korf, U. Increasing the sensitivity of reverse phase protein arrays by antibody-mediated signal amplification. Proteome science. Proteome Sci., 2010, 8.
[73]
Ramachandran, N. Larson, D. N.; Stark, P. R. H.; Hainsworth, E.; LaBaer, J. FEBS J., 2005, 272(21), 5412-5425.
[http://dx.doi.org/10.1111/j.1742-4658.2005.04971.x] [PMID: 16262683 ]
[74]
a)D. W. Unfricht, S. L. Colpitts, S. M. Fernandez, M. A. Lynes, Proteomics, 2005, 5(17), 4432-4442.
b)Z. H. Wang, G. A label-free multisensing immunosensor based on imaging ellipsometry. Jin. Anal. Chem., 2003, 75(22), 6119-6123.
[http://dx.doi.org/10.1021/ac0347258] [PMID: 14615990 ]
[75]
Krizkova, S.; Heger, Z.; Zalewska, M.; Moulick, A.; Adam, V.; Kizek, R. Nanotechnologies in protein microarrays. Nanomedicine (Lond.), 2015, 10(17), 2743-2755.
[http://dx.doi.org/10.2217/nnm.15.81] [PMID: 26039143 ]
[76]
Gavin, I.M.; Kukhtin, A.; Glesne, D.; Schabacker, D.; Chandler, D.P. Analysis of protein interaction and function with a 3-dimensional MALDI-MS protein array. Biotechniques, 2005, 39(1), 99-107.
[http://dx.doi.org/10.2144/05391RR02] [PMID: 16060374 ]
[77]
Sauer, U. Analytical Protein Microarrays: Advancements Towards Clinical Applications. Sensors (Basel), 2017, 17(2), E256.
[http://dx.doi.org/10.3390/s17020256] [PMID: 28146048 ]
[78]
Knezevic, V.; Leethanakul, C.; Bichsel, V.E.; Worth, J.M.; Prabhu, V.V.; Gutkind, J.S.; Liotta, L.A.; Munson, P.J.; Petricoin, E.F., III; Krizman, D.B. Proteomic profiling of the cancer microenvironment by antibody arrays.. Proteomics,, 2001, 1(10), 1271-1278.
[http://dx.doi.org/10.1002/1615-9861(200110)1:10 1271::AID-PROT127 3.0.CO;2-6 ] [PMID: 11721638 ]
[79]
Chen, Z.; Pei, D.; Jiang, L.; Song, Y.; Wang, J.; Wang, H.; Zhou, D.; Zhai, J.; Du, Z.; Li, B.; Qiu, M.; Han, Y.; Guo, Z.; Yang, R. Antigenicity analysis of different regions of the severe acute respiratory syndrome coronavirus nucleocapsid protein. Clin. Chem., 2004, 50(6), 988-995.
[http://dx.doi.org/10.1373/clinchem.2004.031096] [PMID: 15054081 ]
[80]
Schott, C.; Becker, K. F. Guidelines for Molecular Analysis in Archive Tissues, 2011. 279-282.
[81]
a) B. Spurrier, S. Ramalingam, S. Nishizuka Nat. Protoc., 2008, 3(11), 1796-1808.
b) O. H. Negm, A. A. Muftah, M. A. Aleskandarany, M. R. Hamed, D. A. Ahmad, C. C. Nolan, M. Diez-Rodriguez, P. J. Tighe, I. O. Ellis, E. A. Rakha, A. R. Green Breast Cancer Res. Treat., 2016, 155(1), 25-35.
[http://dx.doi.org/10.1007/s10549-015-3654-2] [PMID: 26661092]
[82]
Nishizuka, S.; Charboneau, L.; Young, L.; Major, S.; Reinhold, W.C.; Waltham, M.; Kouros-Mehr, H.; Bussey, K.J.; Lee, J.K.; Espina, V.; Munson, P.J.; Petricoin, E., III; Liotta, L.A.; Weinstein, J.N. Proteomic profiling of the NCI-60 cancer cell lines using new high-density reverse-phase lysate microarrays. Proc. Natl. Acad. Sci. USA, 2003, 100(24), 14229-14234.
[http://dx.doi.org/10.1073/pnas.2331323100] [PMID: 14623978 ]
[83]
Petricoin, E.F., III; Espina, V.; Araujo, R.P.; Midura, B.; Yeung, C.; Wan, X.; Eichler, G.S.; Johann, D.J., Jr; Qualman, S.; Tsokos, M.; Krishnan, K.; Helman, L.J.; Liotta, L.A. Phosphoprotein pathway mapping: Akt/mammalian target of rapamycin activation is negatively associated with childhood rhabdomyosarcoma survival. Cancer Res., 2007, 67(7), 3431-3440.
[http://dx.doi.org/10.1158/0008-5472.CAN-06-1344] [PMID: 17409454]
[84]
Sevecka, M.; MacBeath, G. State-based discovery: a multidimensional screen for small-molecule modulators of EGF signaling. Nat. Methods, 2006, 3(10), 825-831.
[http://dx.doi.org/10.1038/nmeth931] [PMID: 16990815 ]
[85]
Hu, S.H.; Xie, Z.; Qian, J.; Blackshaw, S.; Zhu, H. Functional protein microarray technology. Wires Syst. Biol. Med. (Aligarh), 2011, 3(3), 255-268.
[http://dx.doi.org/10.1002/wsbm.118] [PMID: 20872749]
[86]
Ryan, D.P.; Matthews, J.M. Protein-protein interactions in human disease. Curr. Opin. Struct. Biol., 15(4)2005. , 441-446.
[http://dx.doi.org/10.1016/j.sbi.2005.06.001]
[87]
Ramachandran, N.; Hainsworth, E.; Bhullar, B.; Eisenstein, S.; Rosen, B.; Lau, A.Y.; Walter, J.C.; LaBaer, J. Self-assembling protein microarrays. Science, 2004, 305(5680), 86-90.
[http://dx.doi.org/10.1126/science.1097639] [PMID: 15232106 ]
[88]
Huang, J.; Zhu, H.; Haggarty, S.J.; Spring, D.R.; Hwang, H.; Jin, F.; Snyder, M.; Schreiber, S.L. Finding new components of the target of rapamycin (TOR) signaling network through chemical genetics and proteome chips. Proc. Natl. Acad. Sci. USA, 2004, 101(47), 16594-16599.
[http://dx.doi.org/10.1073/pnas.0407117101] [PMID: 15539461 ]
[89]
Liang, W.; Wang, S.; Festa, F.; Wiktor, P.; Wang, W.; Magee, M.; LaBaer, J.; Tao, N. Measurement of small molecule binding kinetics on a protein microarray by plasmonic-based electrochemical impedance imaging. Anal. Chem., 2014, 86(19), 9860-9865.
[http://dx.doi.org/10.1021/ac5024556] [PMID: 25153794]
[90]
Chen, G.Y.J.; Uttamchandani, M.; Zhu, Q.; Wang, G.; Yao, S.Q. Developing a strategy for activity-based detection of enzymes in a protein microarray. ChemBioChem, 2003, 4(4), 336-339.
[http://dx.doi.org/10.1002/cbic.200390054] [PMID: 12672113 ]
[91]
Lee, M.Y.; Park, C.B.; Dordick, J.S.; Clark, D.S. Metabolizing enzyme toxicology assay chip (MetaChip) for high-throughput microscale toxicity analyses. Proc. Natl. Acad. Sci. USA, 2005, 102(4), 983-987.
[http://dx.doi.org/10.1073/pnas.0406755102] [PMID: 15657119 ]

Rights & Permissions Print Cite
© 2024 Bentham Science Publishers | Privacy Policy